Created
August 9, 2015 19:13
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ggplot2 Caterpillar Plot
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# Load libraries | |
lapply(c("R2MLwiN","arm","ggplot2","RColorBrewer","grid"),library, character.only=TRUE) | |
# Set working directory and load data | |
setwd("~/R") | |
data(tutorial) | |
str(tutorial) | |
# Fit a linear varying intercept multilevel model with group level predictors of normexam ~ sex + standlrt + vrband + schgend + avslrt + schav + (1|school) | |
fit.1 <-lmer(normexam ~ sex + standlrt + vrband + schgend + avslrt + schav + (1|school), data=tutorial) | |
display(fit.1) | |
# Display "Random"/"Varying" i.e. school effects | |
ranef(fit.1) | |
# Extract higher level residuals | |
ranef <-ranef(fit.1) | |
ranef.se<-se.ranef(fit.1) | |
u0mn <-ranef$school | |
u0se <-ranef.se$school | |
# Rank residuals | |
u0rankmn = rank(u0mn) | |
u0hi <- u0mn + (1.96*u0se) | |
u0lo <- u0mn - (1.96*u0se) | |
# Combine into data.frame | |
d <-data.frame(u0mn,u0rankmn, u0hi, u0lo) | |
# Set colors | |
palette <- brewer.pal("Greys", n=9) | |
color.background = palette[1] | |
color.grid.major = palette[5] | |
color.axis.text = palette[6] | |
color.axis.title = palette[7] | |
color.title = palette[9] | |
# Plot | |
k <- ggplot()+ | |
geom_pointrange(data=d,mapping=aes(x=d$u0rankmn, y=d$X.Intercept., ymin=d$X.Intercept..2,ymax=d$X.Intercept..1), position="identity", width=0.5, size=1, color="black")+ | |
theme_bw() + | |
# Set the entire chart region to a light gray color | |
theme(panel.background=element_rect(fill=color.background, color=color.background)) + | |
theme(plot.background=element_rect(fill=color.background, color=color.background)) + | |
theme(panel.border=element_blank(), axis.line=element_line(), axis.line.y=element_blank()) + | |
# Format the grid | |
theme(panel.grid.major=element_line(colour=color.background,size=.75)) + | |
theme(axis.ticks=element_blank()) + | |
theme(axis.line.x =element_line(colour="#535353", size=.75))+ | |
theme(axis.line.y =element_line(colour="#535353", size=.75))+ | |
# Dispose of the legend | |
theme(legend.position="none") + | |
# Set title and axis labels, and format these and tick marks | |
ggtitle("Residuals: Intercept")+ | |
theme(plot.title=element_text(face="bold",hjust=-.08,vjust=2,colour="#3C3C3C",size=20)) + | |
xlab("Rank of residuals") + | |
ylab("Intercept") + | |
theme(axis.text.x=element_text(size=17,colour="#535353",face="bold")) + | |
theme(axis.text.y=element_text(size=17,colour="#535353",face="bold")) + | |
theme(axis.title.y=element_text(size=17,colour="#535353",face="bold",vjust=1.5)) + | |
theme(axis.title.x=element_text(size=17,colour="#535353",face="bold",vjust=-.5)) + | |
# Big bold line at y=0 | |
geom_hline(yintercept=0,size=1.2, alpha=0.7,colour="#EF3B2C", linetype="twodash")+ | |
# Plot margins and finally line annotations | |
theme(plot.margin = unit(c(1, 1, .5, .7), "cm")) |
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